%'time_series': extract a time series, used with series.fig
%------------------------------------------------------------------------
% function GUI_input=time_series(Param)
%
%OUTPUT
% GUI_input=list of options in the GUI series.fig needed for the function
%
%INPUT:
%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
%i2_series: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
%Series: Matlab structure containing information set by the series interface
%
function GUI_input=time_series(Param) 

%% requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
if ~exist('Param','var')
    GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
        'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
        'RootFile';'on';... %root input file name ('on' by default)
        'FileExt';'on';... %input file extension ('on' by default)
        'NomType';'on';...%type of file indexing ('on' by default)
        'NbSlice';'on'; ...%nbre of slices ('off' by default)
        'VelTypeMenu';'two';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default)
        'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
        'CoordType';'on';...%can use a transform function 'off' by default
        'GetObject';'on';...%can use projection object ,'off' by default
        %'GetMask';'on'...%can use mask option   ,'off' by default
        %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter 
               ''};
    return %exit the function 
end

%% input parameters
% read the xml file for batch case
if ischar(Param) && ~isempty(find(regexp('Param','.xml$')))
    Param=xml2struct(Param);
else %  RUN case: parameters introduced as the input structure Param
    hseries=guidata(Param.hseries);%handles of the GUI series
    WaitbarPos=get(hseries.waitbar_frame,'Position');
end
[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);

%% coordinate transform or other user defined transform
transform_fct='';%default
if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'fct_handle')
    transform_fct=Param.FieldTransform.fct_handle;
end

%% projection object
test_object=get(hseries.GetObject,'Value');
if test_object
    hset_object=findobj(allchild(0),'tag','set_object');
    ProjObject=read_GUI(hset_object);
    answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type]);
    if ~isequal(answeryes,'Yes')
        return
    end
else
    msgbox_uvmat('ERROR','a projection object is needed');
    return
end

%% features of the input fields 
RootPath=Param.InputTable(:,1);
RootFile=Param.InputTable(:,3);
% SubDir=Param.InputTable(:,2);
NomType=Param.InputTable(:,4);
FileExt=Param.InputTable(:,5);
% ext=FileExt{1};
% form=imformats(ext(2:end));%test valid Matlab image formats
nbfield=size(i1_series{1},1)*size(i1_series{1},2); %number of fields in the time series

%% determine image type
hhh=which('mmreader');
testnetcdf=0;
nbview=length(RootPath);%Number of input series: this function  accepts only one or two input file series (sub_field is used in the latter case)
for iview=1:nbview
    if isequal(FileExt{iview},'.nc')||isequal(FileExt{iview},'.cdf')
        FileType{iview}='netcdf';
        testnetcdf=1;
    elseif isequal(lower(FileExt{iview}),'.avi')
        if ~isequal(hhh,'')%&& mmreader.isPlatformSupported()
            MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}]));
            FileType{iview}='movie';
        else
            FileType{iview}='avi';
        end
    elseif isequal(lower(FileExt{iview}),'.vol')
        FileType{iview}='vol';
    else 
       form=imformats(FileExt{iview}(2:end));
       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
           if isequal(NomType{iview},'*');
               FileType{iview}='multimage';
           else
               FileType{iview}='image';
           end
       end
    end
end
filebase{1}=fullfile(RootPath{1},RootFile{1});

%% number of slices
NbSlice=Param.NbSlice;

%% Field and velocity type (the same for the two views)
FieldName={''};

if isfield(Param,'InputFields')&&isfield(Param.InputFields,'FieldMenu')  
    FieldName=Param.InputFields.FieldMenu;%the same set of fields for all views
    VelType{1}=Param.InputFields.VelTypeMenu;
end
if isempty(FieldName) && testnetcdf
    msgbox_uvmat('ERROR','A field must be defined as input')
    return
end
if isequal(FieldName,'get_field...')
    hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
    if numel(hget_field)>1
        delete(hget_field(2:end)) % delete multiple occurerence of the GUI get_fioeld
    elseif isempty(hget_field)
        filename=filecell{1,1};
      % filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),num_j2{1}(1),SubDir{1}); 
       idetect(iview)=exist(filename,'file');
       hget_field=get_field(filename);
       return
    end
    SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
    if isempty(SubField)
        delete(hget_field)
        filename=filecell{1,1};
       %filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),j2_series{1}(1),SubDir{1});
        hget_field=get_field(filename);
        SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
    end
end

%% detect whether the two files are 'images' or 'netcdf'
testcivx=0;
% FileExt=get(hseries.FileExt,'String');
if ~isequal(FieldName,{'get_field...'})
    testcivx=isequal(FileType{1},'netcdf');
end
% VelType_str=get(hseries.VelTypeMenu,'String');
% VelType_val=get(hseries.VelTypeMenu,'Value');
% VelType{1}=VelType_str{VelType_val};
% if nbview==2
%     VelType_str=get(hseries.VelTypeMenu_1,'String');
%     VelType_val=get(hseries.VelTypeMenu_1,'Value');
%     VelType{2}=VelType_str{VelType_val};
% end

%% Calibration data and timing: read the ImaDoc files
% mode=''; %default
timecell={};
XmlData={};
itime=0;
NbSlice_calib={};
for iview=1:nbview%Loop on views
    XmlData{iview}=[];%default
    filebase{iview}=fullfile(RootPath{iview},RootFile{iview});
    if exist([filebase{iview} '.xml'],'file')
        [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); 
        if isfield(XmlData{iview},'Time')
            itime=itime+1;
            timecell{itime}=XmlData{iview}.Time;
        end
        if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
            NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
            if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
                msgbox_uvmat('WARNING','inconsistent number of Z indices for the field series');
            end
        end 
    elseif exist([filebase{iview} '.civ'],'file')%old convention .civ text file
        [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']);
        itime=itime+1;
        timecell{itime}=time;
        XmlData{iview}.Time=time;
        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
        GeometryCalib.Tx=0;
        GeometryCalib.Ty=0;
        GeometryCalib.Tz=1;
        GeometryCalib.dpx=1;
        GeometryCalib.dpy=1;
        GeometryCalib.sx=1;
        GeometryCalib.Cx=0;
        GeometryCalib.Cy=0;
        GeometryCalib.f=1;
        GeometryCalib.kappa1=0;
        GeometryCalib.CoordUnit='cm';
        XmlData{iview}.GeometryCalib=GeometryCalib;
        if error==1
            msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
        end
    end
end
time=[];%default
if ~isempty(timecell)
    if numel(timecell{1})<nbfield
       msgbox_uvmat('WARNING','time array from ImaDoc to short')
    else
        time=timecell{1}; %time defined from ImaDoc file (image series)
    end
end

%% check coincidence in time
if length(timecell)>1
    for icell=2:length(timecell)
        if isequal(size(timecell{icell}),size(time))
            diff_time=max(abs(timecell{icell}-time));
            if diff_time>0
                msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)])
                break
            end 
        else
            msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used')
            break
        end
    end
end
if ~isempty(time)
    display(['time is read from ' filebase{iview} '.xml'])
end

%%  Root name of output files (TO GENERALISE FOR TWO INPUT SERIES)
subdir_result='time_series';
pathdir=fullfile(RootPath{1},subdir_result);
while exist(pathdir,'dir')
    subdir_result=[subdir_result '.0'];
    pathdir=fullfile(RootPath{1},subdir_result);
end
[m1,m2,m3]=mkdir(pathdir);
if ~isequal(m2,'')
     msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation
end
[xx,msg2] = fileattrib(pathdir,'+w','g'); %yield writing access (+w) to user group (g)
if ~strcmp(msg2,'')
    msgbox_uvmat('ERROR',['pb of permission for ' pathdir ': ' msg2])%error message for directory creation
    return
end
filebase_out=filebase{1}; 
 i21=i1_series{end}(end);
 if ~isempty(i2_series{end})
     i21=i2_series{end}(end)-i1_series{1}(1);
 end
 j21=1;
 if ~isempty(j1_series{1})
     j21=j1_series{end}(end);
      if ~isempty(j2_series{end})
          j21=j2_series{end}(end)-j21;
      end
 end
NomTypeOut=nomtype2pair(NomType{1},i21,j21);


%% velocity type
VelType_str=get(hseries.VelTypeMenu,'String');
VelType_val=get(hseries.VelTypeMenu,'Value');
VelType{1}=VelType_str{VelType_val};
if nbview==2
    VelType_str=get(hseries.VelTypeMenu_1,'String');
    VelType_val=get(hseries.VelTypeMenu_1,'Value');
    VelType{2}=VelType_str{VelType_val};
end

%% LOOP ON SLICES
nbmissing=0; %number of undetected files
for i_slice=1:NbSlice
    dt=[];
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%  LOOP ON FIELDS WITHIN  A SLICE
    filecounter=0;
    for ifile=i_slice:NbSlice:nbfield
        stopstate=get(hseries.RUN,'BusyAction');
        errormsg='';
        if isequal(stopstate,'queue')% enable STOP command
            update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) % update the waitbar
            % loop on views (in case of multiple input series)
            for iview=1:nbview
                filename=filecell{iview,ifile};
               % filename=name_generator(filebase{iview},...
                %    i1_series{iview}(ifile),j1_series{iview}(ifile),FileExt{iview},NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile),SubDir{iview});
                if exist(filename,'file')
                    try
                        Data{iview}=[]; %default
                        if ~isequal(FileType{iview},'netcdf')
                            Data{iview}.ListVarName={'A'};
                            Data{iview}.AName='image';
                            switch FileType{iview}
                                case 'movie'
                                    A=read(MovieObject{iview},i1_series{iview}(ifile));
                                case 'avi'
                                    mov=aviread(filename,i1_series{iview}(ifile));
                                    A=frame2im(mov(1));
                                case 'vol'
                                    A=imread(filename);
                                case 'multimage'
                                    A=imread(filename,i1_series{iview}(ifile));
                                case 'image'
                                    A=imread(filename);
                            end
                            Data{iview}.ListVarName={'AY','AX','A'}; %
                            npy=size(A,1);
                            npx=size(A,2);
                            nbcolor=size(A,3);
                            if nbcolor==3
                                Data{iview}.VarDimName={'AY','AX',{'AY','AX','rgb'}};
                            else
                                Data{iview}.VarDimName={'AY','AX',{'AY','AX'}};
                            end
                            Data{iview}.AY=[npy-0.5 0.5];
                            Data{iview}.AX=[0.5 npx-0.5];
                            Data{iview}.A=double(A);
                            Data{iview}.CoordUnit='pixel';
                        elseif testcivx
                            [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType);
                            if ~isequal(FieldName,{''})
                                Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..)
                            end
                        else
                            [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data
                            Data{iview}.VarAttribute=SubField.VarAttribute;
                        end
                        if ~isempty(NbSlice_calib)  % z index
                            Data{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1;
                        end
                    catch ME
                        errormsg=ME.message;
                    end
                else
                    errormsg=[filename ' is missing'];
                end
                if isempty(errormsg)
                    % coordinate transform (or other user defined transform)
                    if ~isempty(transform_fct)
                        if nbview==2
                            [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
                            if isempty(Data{2})
                                Data(2)=[];
                            end
                        else
                            Data{1}=transform_fct(Data{1},XmlData{1});
                        end
                    end
                    if length(Data)==2
                        [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields
                    else
                        Field=Data{1};
                    end
                    if test_object
                        [Field,errormsg]=proj_field(Field,ProjObject);
                    end
                end
                filecounter=filecounter+1;
                
                % initiate the time series at the first iteration
                if filecounter==1
                    % stop program if the first field reading is in error
                    if ~isempty(errormsg)
                        msgbox_uvmat('ERROR',['error in time_series/sub_field:' errormsg])
                        return
                    end
                    RecordData=Field;%default
                    RecordData.NbDim=Field.NbDim+1; %add the time dimension for plots
                    nbvar=length(Field.ListVarName);
                    if nbvar==0
                        msgbox_uvmat('ERROR','no input variable selected in get_field')
                        return
                    end
                    testsum=2*ones(1,nbvar);%initiate flag for action on each variable
                    if isfield(Field,'VarAttribute') % look for coordinate and flag variables
                        for ivar=1:nbvar
                            if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role')
                                var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable
                                if isequal(var_role,'errorflag')
                                    msgbox_uvmat('ERROR','do not handle error flags in time series')
                                    return
                                end
                                if isequal(var_role,'warnflag')
                                    testsum(ivar)=0;  % not recorded variable
                                    eval(['RecordData=rmfield(RecordData,''' Field.ListVarName{ivar} ''');']);%remove variable
                                end
                                if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|...
                                        isequal(var_role,'coord_z')|isequal(var_role,'coord')
                                    testsum(ivar)=1; %constant coordinates, record without time evolution
                                end
                            end
                            % check whether the variable ivar is a dimension variable
                            DimCell=Field.VarDimName{ivar};
                            if ischar(DimCell)
                                DimCell={DimCell};
                            end
                            if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables
                                testsum(ivar)=1;
                            end
                        end
                    end
                    for ivar=1:nbvar
                        if testsum(ivar)==2
                            eval(['RecordData.' Field.ListVarName{ivar} '=[];'])
                        end
                    end
                    RecordData.ListVarName=[{'Time'} RecordData.ListVarName];
                end
                
                % add data to the current field
                for ivar=1:length(Field.ListVarName)
                    VarName=Field.ListVarName{ivar};
                    VarVal=Field.(VarName);
                    if testsum(ivar)==2% test for recorded variable
                        if isempty(errormsg)
                            if isequal(ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode
                                if isempty(VarVal)
                                    msgbox_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(ifile))])
                                    return
                                end
                                VarVal=mean(VarVal,1);
                            end
                            VarVal=shiftdim(VarVal,-1); %shift dimension
                            RecordData.(VarName)=cat(1,RecordData.(VarName),VarVal);%concanete the current field to the time series
                        else
                            RecordData.(VarName)=cat(1,RecordData.(VarName),0);% put each variable to 0 in case of input reading error
                        end
                    elseif testsum(ivar)==1% variable representing fixed coordinates
                        eval(['VarInit=RecordData.' VarName ';']);
                        if isempty(errormsg) && ~isequal(VarVal,VarInit)
                            msgbox_uvmat('ERROR',['time series requires constant coordinates ' VarName])
                            return
                        end
                    end
                end
                
                % record the time:
                if isempty(time)% time read in ncfiles
                    if isfield(Field,'Time')
                        RecordData.Time(filecounter,1)=Field.Time;
                    else
                        RecordData.Time(filecounter,1)=ifile;%default
                    end
                else % time from ImaDoc prevails  TODO: correct 
                  %  RecordData.Time(filecounter,1)=time{1}(i1_series{1})(ifile),j1_series{1}(ifile))+time(end,i2_series{end}(ifile),j2_series{end}(ifile)))/2;
                  RecordData.Time(filecounter,1)=i1_series{1}(ifile);% TODO : generalise
                end
                
                % record the number of missing input fields
                if ~isempty(errormsg)
                    nbmissing=nbmissing+1;
                    display(['ifile=' num2str(ifile) ':' errormsg])
                end
            end
        end
    end
    %%%%%%% END OF LOOP WITHIN A SLICE
   
    %remove time for global attributes if exists
    Time_index=find(strcmp('Time',RecordData.ListGlobalAttribute));
    if ~isempty(Time_search)
        RecordData.ListGlobalAttribute(Time_index)=[];
    end
    RecordData.Conventions='uvmat';
%     for iattr=1:numel(RecordData.ListGlobalAttribute)
%         if strcmp(RecordData.ListGlobalAttribute{iattr},'Time')
%             RecordData.ListGlobalAttribute(iattr)=[];
%             break
%         end
%     end
    for ivar=1:numel(RecordData.ListVarName)
        VarName=RecordData.ListVarName{ivar};
        eval(['RecordData.' VarName '=squeeze(RecordData.' VarName ');']) %remove singletons
    end
    
    % add time dimension 
    for ivar=1:length(Field.ListVarName)
        DimCell=Field.VarDimName(ivar);
        if testsum(ivar)==2%variable used as time series
            RecordData.VarDimName{ivar}=[{'Time'} DimCell];
        elseif testsum(ivar)==1
            RecordData.VarDimName{ivar}=DimCell;
        end
    end
    indexremove=find(~testsum);
    if ~isempty(indexremove)
        RecordData.ListVarName(1+indexremove)=[];
        RecordData.VarDimName(indexremove)=[];
        if isfield(RecordData,'Role') && ~isempty(RecordData.Role{1})%generaliser aus autres attributs
            RecordData.Role(1+indexremove)=[];
        end
    end
    
    %shift variable attributes
    if isfield(RecordData,'VarAttribute')
        RecordData.VarAttribute=[{[]} RecordData.VarAttribute];
    end
    RecordData.VarDimName=[{'Time'} RecordData.VarDimName];
    RecordData.Action=Param.Action;%name of the processing programme
    test_time=diff(RecordData.Time)>0;% test that the readed time is increasing (not constant)
    if ~test_time
        RecordData.Time=[1:filecounter];
    end
    
    % display nbmissing
    if ~isequal(nbmissing,0)
        msgbox_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'])
    end
    
    %name of result file
   % [filemean]=...
    %    name_generator(filebase_out,i1_series{1}(i_slice),j1_series{1}(i_slice),'.nc','_i1-i2_j1-j2',1,i2_series{end}(ifile),j2_series{end}(ifile),subdir_result);
    filemean=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},'.nc','_1',i1_series{1}(i_slice));
    errormsg=struct2nc(filemean,RecordData); %save result file
    if isempty(errormsg)
        display([filemean ' written'])
    else
        msgbox_uvmat('ERROR',['error in Series/struct2nc: ' errormsg])
    end
end

%% plot the time series (the last one in case of multislices)
figure
haxes=axes;
plot_field(RecordData,haxes)

%% display the result file using the GUI get_field
hget_field=findobj(allchild(0),'name','get_field');
if ~isempty(hget_field)
    delete(hget_field)
end
get_field(filemean,RecordData)
    
%------------------------------------------------------------------------
% --- Executes on selection change in CoordType.
function CoordType_Callback(hObject, eventdata, handles)
%------------------------------------------------------------------------
menu_str=get(handles.CoordType,'String');
ind_coord=get(handles.CoordType,'Value');
coord_option=menu_str{ind_coord};
if isequal(coord_option,'more...'); 
    fct_name='';
    if exist('./TMP/current_usr_fct.mat','file')% if a file is found
        h=load('./TMP/current_usr_fct.mat');
        if isfield(h,'fct_name'); 
            fct_name=h.fct_name;
        end
    end
    prompt = {'Enter the name of the transform function'};
    dlg_title = 'user defined transform';
    num_lines= 1;
    [FileName, PathName, filterindex] = uigetfile( ...
       {'*.m', ' (*.m)';
        '*.m',  '.m files '; ...
        '*.*', 'All Files (*.*)'}, ...
        'Pick a file', fct_name);
    fct_name=fullfile(PathName,FileName);
    addpath(PathName);%add the path to the selected fct
    [errormsg,date_str]=check_functions;%check whether new functions can oversed the uvmat package A UTILISER
    if ~exist(fct_name,'file')
           warndlg(['image procesing fct ' fct_name ' not found'])
    else
        transform=FileName(1:end-2);% 
        update_menu(handles.CoordType,transform)%add the selected fct to the menu
  %      set(handles.mouse_coord,'String',menu([1:end-1])')%update the mouse coord menu 
      %save ('./TMP/current_usr_fct.mat','fct_name');
    end   
end
ind_coord=get(handles.CoordType,'Value');   

%---------------------------------------------------------------------
% % --- Executes on selection change in ProjObject.
% function ProjObject_Callback(hObject, eventdata, handles)
% 
% list_object=get(handles.ProjObject,'String');
% index=get(handles.ProjObject,'Value');
% hseries=get(handles.ProjObject,'Parent');
% SeriesData=get(hseries,'UserData');
% Obj=SeriesData.ProjObject{index};
% [SeriesData.hset_object,SeriesData.sethandles]=set_object(SeriesData.ProjObject{index});
% set(hseries,'UserData',SeriesData);